qsub returns "no such file or directory error" for few files.

Question

[bubby.bubbles]

Hi,

I am launched a job script with the "qsub" command ,but it returns a error message after being executed for minimal number of seconds .

The error message contains the below :

/var/spool/torque/mom_priv/jobs/1506086.SC: line 10: cd: PWD: No such file or directory Can't open perl script "myscript.pl": No such file or directory

The directory is correct and I have the perl script in it.Actually I have many job scripts running in the same directory.But I am receiving this error only for two perl scripts. Could anyone please help me with the issue.

Thanks!

Answer 1

[Alex Reynolds]

Maybe add -cwd:

 $ man qsub
 ...
 -cwd Available for qsub, qsh, qrsh and qalter only.

      Execute the job from  the  current  working  directory.
      This switch will activate Sun Grid Engine's path alias-
      ing facility, if the corresponding configuration  files
      are present (see sge_aliases(5)).

[bubby.bubbles]

Hi Alex,

Thanks for the response. I have executed the job from the current working directory.I have executed it twice but it returned the same error message twice.Other job scripts that were executed with this are running without any errors.I have tried placing the files in the home directory and another directory and executed qsub but with no luck !

[Alex Reynolds]

I mean add -cwd as an option to your qsub command. This usually helps SGE set up a runtime environment so that it can find files in your current working directory.

[Alex Reynolds]

Your local IT group should be able to assist with troubleshooting this, in any case. Much about SGE is dependent on how the scheduler was set up.

Answer 2

[berge2015]

If by 'PWD' you were directing your pbs script to your working directory, then that could be your problem. I personally prefer writing the full path, as in: cd /home/user/your/working/directory/) and it has always ran smoothly.

Also, it's better to call the script as perl script.pl if the script hasn't been changed to executable.